Wednesday, December 28, 2011

Citing phytools

phytools is quite a new package - I posted the first release of phytools in June, and it has been available through CRAN only since late August. Several phytools functions have been cited already, but the package as a whole has not yet had time to accumulate significant citations (although a few are beginning to trickle in).

I was pleased to find today that the phytools package had been cited in a recent Journal of Experimental Biology article by Grim & colleagues. Unfortunately I was somewhat dismayed to discover that phytools was cited improperly, as follows (p. 3756):

None of the datasets, including enzyme activity, protein level and UI, included a phylogenetic signal [as indicated by Blomberg’s K using the phylogeny published by Takezaki et al. (Takezaki et al., 2003) and the ‘phytools’ package in R (R Development Core Team, 2008); P>0.05].

(In other words, phytools has been attributed to the R Development Core Team, and not to me.)

It is generally very easy to find citation information for any R package that you are using - just type citation("package-name") at the command prompt. So, for phytools this would look something like this:

> citation("phytools")

To cite phytools in publication use:

  Revell, L. J. (In press) phytools: An R package for phylogenetic
  comparative biology (and other things)
  Methods Ecol. Evol. doi:10.1111/j.2041-210X.2011.00169.x

A BibTeX entry for LaTeX users is
...

As phytools is continually evolving, you may want to cite its version number. Find it with 'help(package=phytools)'.


Don't forget, of course, to also cite package dependencies - particularly those on which the functions that you used for your analysis rely; and the R statistical computing environment (as Grim et al. rightly do, above).

1 comment:

  1. Evidently, the DOI on that article is bad so the link above does not work (at least not at present). Here is an alternate link to the article.

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